Contacts of the helix formed by residues 61 - 73 (chain M) in PDB entry 1KFY
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 61 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55M VAL* 4.2 7.6 - - - -
60M ASP* 1.3 90.8 + - - +
62M PHE* 1.3 69.4 + - - +
63M GLU* 2.8 27.4 + - - +
64M TYR* 2.9 31.6 + - - -
65M HIS* 3.3 8.7 + - - +
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Residues in contact with PHE 62 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55M VAL* 4.1 20.7 - - + +
61M SER* 1.3 74.5 - - - +
63M GLU* 1.3 56.8 + - - +
65M HIS 3.5 0.9 + - - +
66M PHE* 2.8 30.2 + - - +
86M VAL* 3.3 37.0 - - + +
87M HIS* 3.0 55.2 - + + +
90M PRO* 4.5 12.8 - - + -
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Residues in contact with GLU 63 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61M SER* 2.8 15.7 + - - +
62M PHE* 1.3 77.0 - - - +
64M TYR* 1.3 56.8 + - + +
66M PHE* 3.0 34.1 + - - +
67M HIS* 2.7 40.3 + - + +
572M THR* 5.0 8.9 - - - +
573M LEU* 5.6 5.4 - - - +
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Residues in contact with TYR 64 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59M HIS 4.3 8.1 - - - -
60M ASP* 3.4 14.6 - - - -
61M SER* 2.9 42.8 + - - +
63M GLU* 1.3 80.3 - - + +
65M HIS* 1.3 63.4 + - - +
67M HIS* 3.1 8.7 + + + +
68M ASP* 2.9 28.3 + - - +
121M ILE* 4.9 9.9 - - + -
123M ARG* 3.4 18.4 - - - +
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Residues in contact with HIS 65 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53M ALA* 4.2 14.9 - - + +
54M ALA 4.8 0.2 - - - -
55M VAL* 4.2 16.1 + - + +
61M SER 3.3 3.6 + - - -
62M PHE 3.9 5.6 - - - +
64M TYR* 1.3 79.3 - - - +
66M PHE* 1.3 55.0 + - - +
68M ASP* 3.6 1.3 + - - -
69M THR* 2.4 40.8 + - - -
85M PHE* 3.8 18.4 - + - -
86M VAL* 3.8 16.9 - - + +
89M CYS* 4.1 13.6 - - - -
119M MET* 4.4 1.3 - - - -
123M ARG* 3.5 40.2 - - - +
391M LEU* 4.0 10.5 - - + -
394M ASN* 3.0 31.7 + - - -
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Residues in contact with PHE 66 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62M PHE 2.8 19.8 + - - +
63M GLU* 3.1 30.3 - - - +
65M HIS* 1.3 77.4 - - - +
67M HIS* 1.3 62.9 + - - +
69M THR* 3.3 4.5 + - - -
70M VAL* 3.1 35.0 + - + +
79M GLN* 3.3 48.2 - - + -
82M VAL* 3.2 27.8 - - + -
83M ASP* 3.5 22.2 - - + -
86M VAL* 3.8 8.9 - - + +
571M THR* 4.9 2.9 - - + -
572M THR* 4.0 25.4 - - + -
573M LEU* 4.9 7.9 - - + -
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Residues in contact with HIS 67 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63M GLU* 2.7 20.4 + - + +
64M TYR* 3.4 12.8 - + + +
66M PHE* 1.3 75.9 - - - +
68M ASP* 1.3 67.3 - - - +
70M VAL* 3.2 1.7 + - - +
71M ALA* 2.8 44.4 + - + +
75M TRP* 5.2 7.2 - + - -
573M LEU* 3.2 37.7 - - + +
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Residues in contact with ASP 68 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64M TYR* 2.9 20.7 + - - +
65M HIS* 3.9 6.1 - - - +
67M HIS* 1.3 85.9 - - - +
69M THR* 1.3 57.8 + - - +
71M ALA* 4.0 4.8 - - - +
72M GLY* 3.0 23.2 + - - -
119M MET* 3.7 20.2 - - + +
120M LYS* 4.0 8.6 + - - +
123M ARG* 3.3 24.3 + - - -
391M LEU* 3.3 28.9 - - + +
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Residues in contact with THR 69 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65M HIS* 2.4 37.4 + - - -
66M PHE 3.5 5.2 - - - -
67M HIS 3.2 0.2 - - - -
68M ASP* 1.3 77.1 - - - +
70M VAL* 1.3 57.1 + - - +
72M GLY* 4.0 0.3 - - - -
73M GLY* 3.0 21.0 + - - -
77M CYS* 3.5 7.4 - - - -
82M VAL* 3.6 21.2 - - + +
85M PHE* 5.1 0.6 - - + -
86M VAL* 4.5 1.7 - - - +
385M LEU* 3.4 29.4 - - + +
386M HIS* 4.9 2.4 - - - +
389M ASN 5.0 1.0 - - - +
391M LEU* 3.7 12.1 - - + +
394M ASN* 3.7 18.6 + - - +
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Residues in contact with VAL 70 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66M PHE* 3.1 30.2 + - + +
67M HIS 3.7 4.3 - - - +
69M THR* 1.3 72.2 - - - +
71M ALA* 1.3 65.2 + - - +
73M GLY* 3.1 9.4 + - - -
74M ASP 3.1 9.7 + - - -
75M TRP* 3.1 53.9 + - + +
77M CYS* 4.1 10.0 - - + -
79M GLN* 3.6 30.5 - - + +
82M VAL* 4.5 7.4 - - + -
573M LEU* 4.2 13.9 - - + -
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Residues in contact with ALA 71 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67M HIS* 2.8 32.6 + - + +
68M ASP* 4.0 4.9 - - - +
70M VAL* 1.3 72.6 - - - +
72M GLY* 1.3 58.9 + - - +
74M ASP* 2.8 27.9 + - - +
75M TRP* 4.0 24.6 - - + -
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Residues in contact with GLY 72 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68M ASP 3.0 17.0 + - - -
69M THR 4.0 1.1 - - - -
71M ALA* 1.3 79.6 - - - +
73M GLY* 1.3 57.1 + - - +
74M ASP* 3.2 3.2 + - - +
389M ASN* 2.9 34.0 + - - +
391M LEU* 4.8 9.4 - - - -
530M GLY* 5.4 0.2 - - - -
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Residues in contact with GLY 73 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69M THR 3.0 10.1 + - - -
70M VAL 3.1 3.6 + - - -
71M ALA 3.0 1.6 - - - -
72M GLY* 1.3 76.0 - - - +
74M ASP* 1.3 69.8 + - - +
75M TRP 3.3 2.9 - - - -
76M LEU 3.4 7.4 + - - -
77M CYS* 3.6 9.9 - - - -
386M HIS 3.3 24.0 - - - -
387M GLY 3.7 0.2 - - - -
388M ALA* 2.8 24.9 + - - +
389M ASN 3.6 1.3 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il